Here is my list of the most useful plugins that I’ve found to rely on when creating complex websites with WordPress.
With the ACF plugin, I can declare custom post types in my functions.php and with this plugin attach very cool custom fields to them. This makes it a lot easier than creating meta boxes and custom fields by hand.
The UpThemes Framework makes it very easy to create options pages for your site. It has a clear documentation to help you integrate it.
"Category Order and Taxonomy Terms Order" is THE easiest plugin I’ve found to reorder taxonomies.
"Post types order" is a very useful plugin to reorder any conceivable custom post type. It works like a charm.
A bit more technical
Ever tried to work locally on a website, just to find out that deploying your website’s database was a huge pain because WordPress (and lots of plugins) stores all those absolute URLs in the DB? "WP Migrate DB" make it easy to find & replace every occurrence of these URLs and your site’s path on the file system.
"Debug Bar" is a must. It’s like FireBug, but for WordPress. Easy to install, easy to use. It lets you see interesting details such as the matched rewrite rule for the current page. With the SAVEQUERIES constant set to true (in your wp-config.php file), it also lists all the SQL queries that were performed to display the current page you’re on.